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Snashall CM, Sutton CW, Faro LL, Ceresa C, Ploeg R, Shaheed SU. Comparison of in-gel and in-solution proteolysis in the proteome profiling of organ perfusion solutions. Clin Proteomics 2023; 20:51. [PMID: 37968584 PMCID: PMC10648346 DOI: 10.1186/s12014-023-09440-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/25/2023] [Indexed: 11/17/2023] Open
Abstract
PURPOSE The organ perfusion solution (perfusate), collected at clinically and temporally significant stages of the organ preservation and transplantation process, provides a valuable insight into the biological status of an organ over time and prior to reperfusion (transplantation) in the recipient. The objective of this study was to assess two bottom-up proteomics workflows for the extraction of tryptic peptides from the perfusate. EXPERIMENTAL DESIGN Two different kinds of perfusate samples from kidney and liver trials were profiled using liquid chromatography-mass spectrometry (LC-MS/MS). The preparation of clean peptide mixtures for downstream analysis was performed considering different aspects of sample preparation; protein estimation, enrichment, in-gel and urea-based in-solution digestion. RESULTS In-solution digestion of perfusate allowed identification of the highest number of peptides and proteins with greater sequence coverage and higher confidence data in kidney and liver perfusate. Key pathways identified by gene ontology analysis included complement, coagulation and antioxidant pathways, and a number of biomarkers previously linked to ischemia-reperfusion injury were also observed in perfusate. CONCLUSIONS This study showed that in-solution digestion is a more efficient method for LC-MS/MS analysis of kidney and liver organ perfusion solutions. This method is also quicker and easier than in-gel digestion, allowing for greater sample throughput, with fewer opportunities for experimental error or peptide loss.
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Affiliation(s)
- Corinna M Snashall
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Chris W Sutton
- Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Letizia Lo Faro
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Carlo Ceresa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Rutger Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Leiden University Medical Centre, Leiden University, Leiden, Netherlands
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Sadr Ul Shaheed
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
- NHSBT Oxford Blood Donor Centre John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9BQ, UK.
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2
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Zhao L, Yang Q, Guo W, Zhang F, Yu K, Yang C, Qu F. Non-stoichiometric cobalt sulfide nanodots enhance photothermal and chemodynamic therapies against solid tumor. J Colloid Interface Sci 2021; 600:390-402. [PMID: 34023700 DOI: 10.1016/j.jcis.2021.05.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/18/2021] [Accepted: 05/10/2021] [Indexed: 01/15/2023]
Abstract
Photodynamic therapy (PDT) mainly relies on reactive oxygen species generated by light- activated photosensitizers and oxygen to kill tumor cells. However, a critical limitation of the current PDT is that it is less effective in solid tumors where the microenvironment is hypoxic, and, therefore, repeated treatment is required. Here, non-stoichiometric Co2.19S4 nanodots (NDs), which can be rapidly degraded to cobalt (Co2+) and sulfur (S2-) ions, were developed to enhance tumor photothermal therapy (PTT) and chemodynamic therapy (CDT) via the capture of copper (Cu2+) ions (starvation therapy) in the hypoxic tumor microenvironment under near-infrared irradiation. Co2.19S4 NDs with excellent photothermal conversion efficiency (ɳ = 52%) can be used for PTT, and the Co2+ ions produced by their degradation can catalyze the endogenous hydrogen peroxide of tumor cells to produce highly toxic hydroxyl radicals to achieve tumor CDT. The mechanism of starvation therapy was explored using western blotting, and the results indicated that blocking the uptake of Cu2+ ions could restrain the growth and proliferation of tumors by inhibiting the BRAF/mitogen-activated extracellular signal regulated kinase (MEK)/extracellular regulated protein kinases (ERK) signaling pathway. Our work highlights the great potential of Co2.19S4 NDs as a theranostic agent for implementing photoacoustic/photothermal imaging and starvation therapy-enhanced PTT/CDT.
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Affiliation(s)
- Le Zhao
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, Heilongjiang 150025, China
| | - Qingzhu Yang
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Wei Guo
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, Heilongjiang 150025, China; Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, Heilongjiang 150025, China.
| | - Feng Zhang
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, Heilongjiang 150025, China
| | - Kai Yu
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, Heilongjiang 150025, China
| | - Chunyu Yang
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, Heilongjiang 150025, China.
| | - Fengyu Qu
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, Heilongjiang 150025, China.
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3
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Tripathi A, Kashyap A, Tripathi G, Yadav J, Bibban R, Aggarwal N, Thakur K, Chhokar A, Jadli M, Sah AK, Verma Y, Zayed H, Husain A, Bharti AC, Kashyap MK. Tumor reversion: a dream or a reality. Biomark Res 2021; 9:31. [PMID: 33958005 PMCID: PMC8101112 DOI: 10.1186/s40364-021-00280-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Reversion of tumor to a normal differentiated cell once considered a dream is now at the brink of becoming a reality. Different layers of molecules/events such as microRNAs, transcription factors, alternative RNA splicing, post-transcriptional, post-translational modifications, availability of proteomics, genomics editing tools, and chemical biology approaches gave hope to manipulation of cancer cells reversion to a normal cell phenotype as evidences are subtle but definitive. Regardless of the advancement, there is a long way to go, as customized techniques are required to be fine-tuned with precision to attain more insights into tumor reversion. Tumor regression models using available genome-editing methods, followed by in vitro and in vivo proteomics profiling techniques show early evidence. This review summarizes tumor reversion developments, present issues, and unaddressed challenges that remained in the uncharted territory to modulate cellular machinery for tumor reversion towards therapeutic purposes successfully. Ongoing research reaffirms the potential promises of understanding the mechanism of tumor reversion and required refinement that is warranted in vitro and in vivo models of tumor reversion, and the potential translation of these into cancer therapy. Furthermore, therapeutic compounds were reported to induce phenotypic changes in cancer cells into normal cells, which will contribute in understanding the mechanism of tumor reversion. Altogether, the efforts collectively suggest that tumor reversion will likely reveal a new wave of therapeutic discoveries that will significantly impact clinical practice in cancer therapy.
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Affiliation(s)
- Avantika Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India
| | - Anjali Kashyap
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Greesham Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India
| | - Joni Yadav
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Rakhi Bibban
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Nikita Aggarwal
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Kulbhushan Thakur
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Arun Chhokar
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Mohit Jadli
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Ashok Kumar Sah
- Department of Medical Laboratory Technology, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), India
- Department of Pathology and Laboratory Medicine, Medanta-The Medicity, Haryana, Gurugram, India
| | - Yeshvandra Verma
- Department of Toxicology, C C S University, Meerut, UP, 250004, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Amjad Husain
- Centre for Science & Society, Indian Institute of Science Education and Research (IISER), Bhopal, India
- Innovation and Incubation Centre for Entrepreneurship (IICE), Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Alok Chandra Bharti
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India.
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India.
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India.
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Potential predictive value of cofilin-1 for metastasis occurrence in a small cohort of Argentinian patients with mid-low Breslow thickness melanoma. Pathol Res Pract 2019; 215:152582. [DOI: 10.1016/j.prp.2019.152582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/26/2019] [Accepted: 08/03/2019] [Indexed: 01/11/2023]
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5
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Bracalente C, Rinflerch AR, Ibañez IL, García FM, Volonteri V, Galimberti GN, Klamt F, Durán H. Cofilin-1 levels and intracellular localization are associated with melanoma prognosis in a cohort of patients. Oncotarget 2018; 9:24097-24108. [PMID: 29844875 PMCID: PMC5963619 DOI: 10.18632/oncotarget.25303] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 04/05/2018] [Indexed: 12/11/2022] Open
Abstract
Melanoma is an aggressive cancer with highly metastatic ability. We propose cofilin-1, a key protein in the regulation of actin dynamics and migration, as a prognostic marker. We determined cofilin-1 levels in a retrospective cohort of patients with melanomas and benign lesions of melanocytes (nevi) by immunohistochemistry. Higher cofilin-1 levels were found in malignant melanoma (MM) with Breslow Index (BI)>2 vs MM with BI<2, melanoma in situ (MIS) and nevi and also in MM with metastasis vs MM without detected metastasis. Kaplan-Meier survival curves were performed, clustering patients according to either the type of melanocytic lesions or cofilin-1 level. Survival curves demonstrated worse prognosis of patients with high vs low cofilin-1 levels. TCGA database analysis of melanoma also showed low survival in patients with upregulated cofilin-1 mRNA vs patients without alteration in CFL1 mRNA expression. As cofilin-1 has a dual function depending on its intracellular localization, we evaluated nuclear and cytoplasmic levels of cofilin-1 in melanoma and nevi samples by immunofluorescence. MM with high Breslow index and metastatic cells not only presented cytoplasmic cofilin-1, but also showed this protein at the nucleus. An increase in nuclear/cytoplasmic cofilin-1 mean fluorescence ratio was observed in MM with BI>2 vs MM with BI<2, MIS and nevi. In conclusion, an association of cofilin-1 levels with malignant features and an inverse correlation with survival were demonstrated. Moreover, this study suggests that not only the higher levels of cofilin-1, but also its nuclear localization can be proposed as marker of worse outcome of patients with melanoma.
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Affiliation(s)
- Candelaria Bracalente
- Gerencia de Investigación y Aplicaciones, Comisión Nacional de Energía Atómica, (B1650KNA) San Martín, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, (C1425FQB) CABA, Buenos Aires, Argentina
| | - Adriana R Rinflerch
- Dermatología Experimental, Servicio de Dermatología, Hospital Italiano de Buenos Aires, (C1199ABB) CABA, Buenos Aires, Argentina
| | - Irene L Ibañez
- Gerencia de Investigación y Aplicaciones, Comisión Nacional de Energía Atómica, (B1650KNA) San Martín, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, (C1425FQB) CABA, Buenos Aires, Argentina
| | - Francisco M García
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, Campus Miguelete, (B1650HMP) San Martín, Buenos Aires, Argentina
| | - Victoria Volonteri
- Servicio de Anatomía Patológica, Hospital Italiano de Buenos Aires, (C1199ABB) CABA, Buenos Aires, Argentina
| | - Gastón N Galimberti
- Dermatología Experimental, Servicio de Dermatología, Hospital Italiano de Buenos Aires, (C1199ABB) CABA, Buenos Aires, Argentina
| | - Fabio Klamt
- Laboratório de Bioquímica Celular, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, (90035 003), Porto Alegre, Brazil
| | - Hebe Durán
- Gerencia de Investigación y Aplicaciones, Comisión Nacional de Energía Atómica, (B1650KNA) San Martín, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, (C1425FQB) CABA, Buenos Aires, Argentina.,Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, Campus Miguelete, (B1650HMP) San Martín, Buenos Aires, Argentina
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6
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Filipe EC, Chitty JL, Cox TR. Charting the unexplored extracellular matrix in cancer. Int J Exp Pathol 2018; 99:58-76. [PMID: 29671911 DOI: 10.1111/iep.12269] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/26/2018] [Indexed: 12/12/2022] Open
Abstract
The extracellular matrix (ECM) is present in all solid tissues and considered a master regulator of cell behaviour and phenotype. The importance of maintaining the correct biochemical and biophysical properties of the ECM, and the subsequent regulation of cell and tissue homeostasis, is illustrated by the simple fact that the ECM is highly dysregulated in many different types of disease, especially cancer. The loss of tissue ECM homeostasis and integrity is seen as one of the hallmarks of cancer and typically defines transitional events in progression and metastasis. The vast majority of cancer studies place an emphasis on exploring the behaviour and intrinsic signalling pathways of tumour cells. Their goal was to identify ways to target intracellular pathways regulating cancer. Cancer progression and metastasis are powerfully influenced by the ECM and thus present a vast, unexplored repository of anticancer targets that we are only just beginning to tap into. Deconstructing the complexity of the tumour ECM landscape and identifying the interactions between the many cell types, soluble factors and extracellular-matrix proteins have proved challenging. Here, we discuss some of the emerging tools and platforms being used to catalogue and chart the ECM in cancer.
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Affiliation(s)
- Elysse C Filipe
- Cancer Division, Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, New South Wales, Australia
| | - Jessica L Chitty
- Cancer Division, Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, New South Wales, Australia
| | - Thomas R Cox
- Cancer Division, Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, New South Wales, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
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7
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Pappa KI, Lygirou V, Kontostathi G, Zoidakis J, Makridakis M, Vougas K, Daskalakis G, Polyzos A, Anagnou NP. Proteomic Analysis of Normal and Cancer Cervical Cell Lines Reveals Deregulation of Cytoskeleton-associated Proteins. Cancer Genomics Proteomics 2018. [PMID: 28647699 DOI: 10.21873/cgp.20036] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Both HPV-positive and -negative cervical cancers are primarily associated with features of cell cycle and cytoskeletal disruption; however, the actual biological processes affected remain elusive. To this end, we systematically characterized the intracellular proteomic profiles of four distinct and informative cervical cell lines. MATERIALS AND METHODS Cell extracts from a normal cervical (HCK1T) and three cervical cancer cell lines, one HPV-negative (C33A), and two HPV-positive, SiHa (HPV16+) and HeLa (HPV18+), were analyzed by 2-dimensional electrophoresis and differentially expressed proteins were identified by MALDI-TOF mass spectrometry, while differential expression was confirmed by western blot analysis. RESULTS In total, 113 proteins were found differentially expressed between the normal and the cervical cancer lines. Bioinformatics analysis revealed the actin cytoskeleton signaling pathway to be significantly affected, while up-regulation of cofilin-1, an actin depolymerizing factor, was documented and further validated by western blotting. Furthermore, two-way comparisons among the four cell lines, revealed a set of 18 informative differentially expressed proteins. CONCLUSION These novel identified proteins provide the impetus for further functional studies to dissect the mechanisms operating in the two distinct pathways of cervical carcinogenesis.
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Affiliation(s)
- Kalliopi I Pappa
- First Department of Obstetrics and Gynecology, University of Athens School of Medicine, Alexandra Hospital, Athens, Greece .,Cell and Gene Therapy Laboratory, Centre of Basic Research II, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Vasiliki Lygirou
- Biotechnology Division, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece.,Laboratory of Biology, University of Athens School of Medicine, Athens, Greece
| | - Georgia Kontostathi
- Biotechnology Division, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece.,Laboratory of Biology, University of Athens School of Medicine, Athens, Greece
| | - Jerome Zoidakis
- Biotechnology Division, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Manousos Makridakis
- Biotechnology Division, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Konstantinos Vougas
- Biotechnology Division, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - George Daskalakis
- First Department of Obstetrics and Gynecology, University of Athens School of Medicine, Alexandra Hospital, Athens, Greece
| | - Alexander Polyzos
- Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Nicholas P Anagnou
- Cell and Gene Therapy Laboratory, Centre of Basic Research II, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece.,Laboratory of Biology, University of Athens School of Medicine, Athens, Greece
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8
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Dettling S, Stamova S, Warta R, Schnölzer M, Rapp C, Rathinasamy A, Reuss D, Pocha K, Roesch S, Jungk C, Warnken U, Eckstein V, Grabe N, Schramm C, Weigand MA, von Deimling A, Unterberg A, Beckhove P, Herold-Mende C. Identification of CRKII, CFL1, CNTN1, NME2, and TKT as Novel and Frequent T-Cell Targets in Human IDH-Mutant Glioma. Clin Cancer Res 2018; 24:2951-2962. [PMID: 29563135 DOI: 10.1158/1078-0432.ccr-17-1839] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/23/2017] [Accepted: 03/15/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Successful immunotherapies for IDHmut gliomas require better knowledge of T-cell target antigens. Here, we elucidated their antigen repertoire recognized by spontaneous T-cell responses using an unbiased proteomic approach.Experimental Design: Protein fractionations of tissue lysates from IDHmut gliomas (n = 4) were performed. Fractions were tested by IFNγ ELISpot assay for recognition through patients' T cells. Proteins of immunogenic fractions were identified by mass spectrometry and validated by in silico-predicted synthetic long peptides in patients of origin, additional IDHmut glioma patients (n = 16), and healthy donors (n = 13). mRNA and protein expression of immunogenic antigens was analyzed in tumor tissues and IDHmut glioma stem-like cells (GSC). HLA-A*02-restricted T-cell epitopes were functionally determined by short peptides and numbers of antigen-specific T cells by HLA-peptide tetramer analysis.Results: A total of 2,897 proteins were identified in immunogenic tumor fractions. Based on a thorough filter process, 79 proteins were selected as potential T-cell antigens. Twenty-six of these were recognized by the patients' T cells, and five of them (CRKII, CFL1, CNTN1, NME2, and TKT) in up to 56% unrelated IDHmut glioma patients. Most immunogenic tumor-associated antigens (TAA) were expressed in IDHmut gliomas and GSCs, while being almost absent in normal brain tissues. Finally, we identified HLA-A*02-restricted epitopes for CRKII, NME2, and TKT that were recognized by up to 2.82% of antigen-specific peripheral cytotoxic T cells in IDHmut glioma patients.Conclusions: By analyzing the repertoire of T-cell target antigens in IDHmut glioma patients, we identified five novel immunogenic TAAs and confirmed their expression on IDHmut tumors and GSCs. Clin Cancer Res; 24(12); 2951-62. ©2018 AACR.
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Affiliation(s)
- Steffen Dettling
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Slava Stamova
- Regensburg Center for Interventional Immunology (RCI) and University Medical Center of Regensburg, Regensburg, Germany
| | - Rolf Warta
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carmen Rapp
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Anchana Rathinasamy
- Regensburg Center for Interventional Immunology (RCI) and University Medical Center of Regensburg, Regensburg, Germany
| | - David Reuss
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), CCU Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kolja Pocha
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Saskia Roesch
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Christine Jungk
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Eckstein
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Niels Grabe
- Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University of Heidelberg, Heidelberg, Germany
| | - Christoph Schramm
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus A Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), CCU Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas Unterberg
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Philipp Beckhove
- Regensburg Center for Interventional Immunology (RCI) and University Medical Center of Regensburg, Regensburg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany.
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9
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Yan Z, Yan R. Exploring the Potential of Data-Independent Acquisition Proteomics Using Untargeted All-Ion Quantitation: Application to Tumor Subtype Diagnosis. Anal Chem 2018. [PMID: 29522333 DOI: 10.1021/acs.analchem.7b03920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Maximizing the recovery of meaningful biological information can facilitate proteomics-guided early detection and precise treatment of diseases. However, the conventional protein and peptide level targeted quantification of untargeted data independent acquisition (DIA) such as sequential window acquisition of all theoretical spectra (SWATH) is not necessarily descriptive of all information. Untargeted all-ion quantification theoretically could retrieve more features in SWATH digital maps by circumventing the initial identification process but is intrinsically susceptible to errors because of the extreme complexity of proteome samples and the poor selectivity of a single ion. In this study, we optimized and applied the untargeted all-ion quantification of SWATH data to differentiate tumor subtypes. Large peptides and low abundant peptides benefited more from untargeted all-ion quantification. Top-ranked significant ions were linked to their corresponding ion envelops, where multiple correlated ions were used for measurement and only ion envelopes containing at least three ions with consistent intensity ratio were kept as refined differentiating features. Multivariate statistical analysis revealed that for the tested data set, the refined markers discovered by untargeted SWATH analysis showed comparable diagnostic power to protein and peptide markers. Limitations and benefits of the approach are further discussed.
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Affiliation(s)
- Zhixiang Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences , University of Macau , Taipa, Macao , China.,Zhuhai UM Science & Technology Research Institute , Zhuhai 519080 , China
| | - Ru Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences , University of Macau , Taipa, Macao , China.,Zhuhai UM Science & Technology Research Institute , Zhuhai 519080 , China
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10
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Sun WY, Choi J, Cha YJ, Koo JS. Evaluation of the Expression of Amine Oxidase Proteins in Breast Cancer. Int J Mol Sci 2017; 18:ijms18122775. [PMID: 29261141 PMCID: PMC5751373 DOI: 10.3390/ijms18122775] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 12/15/2017] [Accepted: 12/15/2017] [Indexed: 12/25/2022] Open
Abstract
We aimed to evaluate the expression of amine oxidase proteins in breast cancer and their clinical implications. We performed immunohistochemical staining of amine oxidase proteins (LOX, lysyl oxidase, AOC3, amine oxidase, MAOA, monoamine oxidase A, MAOB, monoamine oxidase B). Based on their hormone receptors, such as estrogen receptor (ER) and progesterone receptor (PR), human epidermal growth factor receptor 2 (HER-2), and Ki-67 immunohistochemical staining, breast cancer was divided into four molecular subtypes: luminal A, luminal B, HER-2 type, and triple-negative breast cancer (TNBC). Luminal A was observed in 380 cases (49.4%), luminal B in 224 (29.1%), HER-2 type in 68 (8.8%), and TNBC in 98 (12.7%). Stromal AOC3, MAO-A, and MAO-B expression varied according to molecular subtypes. Stromal AOC3 expression was high in luminal B and HER-2 type and MAO-A expression was high in luminal A and luminal B (p < 0.001). MAO-B expression was higher in TNBC than in other subtypes (p = 0.020). LOX positivity was associated with high histological grade (p < 0.001) and high Ki-67 labeling index (LI) (p = 0.009), and stromal AOC3 positivity was associated with high histological grade (p = 0.001), high Ki-67 LI (p < 0.001), and HER-2 positivity (p = 0.002). MAO-A positivity was related to low histological grade (p < 0.001), ER positivity, PR positivity (p < 0.001), and low Ki-67 LI (p < 0.001). In univariate analysis, MAO-A positivity was related to short disease-free survival in HER-2 type (p = 0.013), AOC3 negativity was related to short disease-free survival and overall survival in ER-positive breast cancer, PR-positive breast cancer, HER-2-negative breast cancer, and lymph node metastasis. In conclusion, the expression of amine oxidase proteins varies depending on the molecular subtype of breast cancer. Stromal AOC3 expression was high in luminal B and HER-2 type, and MAO-A expression was high in luminal A and luminal B.
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/enzymology
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal/enzymology
- Carcinoma, Ductal/genetics
- Carcinoma, Ductal/metabolism
- Carcinoma, Ductal/pathology
- Female
- Humans
- Middle Aged
- Monoamine Oxidase/genetics
- Monoamine Oxidase/metabolism
- Protein-Lysine 6-Oxidase/genetics
- Protein-Lysine 6-Oxidase/metabolism
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Receptors, Estrogen/genetics
- Receptors, Estrogen/metabolism
- Receptors, Progesterone/genetics
- Receptors, Progesterone/metabolism
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Affiliation(s)
- Woo Young Sun
- Department of Surgery, Daejeon St. Mary's Hospital, College of Medicine, The Cathololic University of Korea, Seoul 06591, Korea.
| | - Junjeong Choi
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21988, Korea.
| | - Yoon Jin Cha
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, Korea.
| | - Ja Seung Koo
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, Korea.
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11
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Liu F, Meng H, Fitzgerald MC. Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins Using SILAC-SPROX. J Proteome Res 2017; 16:3277-3286. [PMID: 28673085 DOI: 10.1021/acs.jproteome.7b00283] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteomic methods for disease state characterization and biomarker discovery have traditionally utilized quantitative mass spectrometry methods to identify proteins with altered expression levels in disease states. Here we report on the large-scale use of protein folding stability measurements to characterize different subtypes of breast cancer using the stable isotope labeling with amino acids in cell culture and stability of proteins from rates of oxidation (SILAC-SPROX) technique. Protein folding stability differences were studied in a comparison of two luminal breast cancer subtypes, luminal-A and -B (i.e., MCF-7 and BT-474 cells, respectively), and in a comparison of a luminal-A and basal subtype of the disease (i.e., MCF-7 and MDA-MB-468 cells, respectively). The 242 and 445 protein hits identified with altered stabilities in these comparative analyses included a large fraction with no significant expression level changes. This suggests thermodynamic stability measurements create a new avenue for protein biomarker discovery. A number of the identified protein hits are known from other biochemical studies to play a role in tumorigenesis and cancer progression. This not only substantiates the biological significance of the protein hits identified using the SILAC-SPROX approach, but it also helps elucidate the molecular basis for their disregulation and/or disfunction in cancer.
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Affiliation(s)
- Fang Liu
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - He Meng
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
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12
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Identification of CD14 as a potential biomarker of hepatocellular carcinoma using iTRAQ quantitative proteomics. Oncotarget 2017; 8:62011-62028. [PMID: 28977922 PMCID: PMC5617482 DOI: 10.18632/oncotarget.18782] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 05/14/2017] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors without effective diagnostic biomarkers. This study intended to dynamically analyze serum proteomics in different pathological stages of liver diseases, and discover potential diagnostic biomarkers for early HCC. Patients with hepatitis B virus (HBV) infection, liver cirrhosis (LC), or HCC together with healthy controls (HC) were enrolled. Proteins differentially expressed between groups were screened using isobaric tagging for relative and absolute quantitation (iTRAQ), and promising HCC biomarker candidates were subjected to bioinformatics analysis, including K-means clustering, gene ontology (GO) and string network analysis. Potential biomarkers were validated by Western blotting and enzyme-linked immunosorbent assay (ELISA), and their diagnostic performance was evaluated using receiver operating characteristic (ROC) curve analysis. Finally, 93 differentially expressed proteins were identified, of which 43 differed between HBV and HC, 70 between LC and HC, and 51 between HCC and HC. Expression levels of gelsolin (GELS) and sulfhydryl oxidase 1 (QSOX1) varied with disease state as follows: HC < HBV < LC < HCC. The reverse trend was observed with CD14. These iTRAQ results were confirmed by Western blotting and ELISA. Logistic regression and ROC curve analysis identified the optimal cut-off for alpha-fetoprotein (AFP), CD14 and AFP/CD14 was 191.4 ng/mL (AUC 0.646, 95%CI 0.467-0.825, sensitivity 31.6%, specificity 94.4%), 3.16 ng/mL (AUC 0.760, 95%CI 0.604-0.917, sensitivity 94.7%, specificity 50%) and 0.197 ng/mL (AUC 0.889, 95%CI 0.785-0.993, sensitivity 84.2%, specificity 83.3%) respectively. In conclusion, Assaying CD14 levels may complement AFP measurement for early detection of HCC.
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13
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Maimaiti Y, Tan J, Liu Z, Guo Y, Yan Y, Nie X, Huang B, Zhou J, Huang T. Overexpression of cofilin correlates with poor survival in breast cancer: A tissue microarray analysis. Oncol Lett 2017; 14:2288-2294. [PMID: 28781665 PMCID: PMC5530183 DOI: 10.3892/ol.2017.6413] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 04/28/2017] [Indexed: 12/20/2022] Open
Abstract
Cofilin, a key regulator of actin cytoskeleton dynamics, is considered to be involved in cellular migration, tumor invasion and mitosis, and its activity is increased in cancer cells. To address the association between cofilin and breast cancer prognosis, which is unclear at present, cofilin expression was analyzed in tissue microarrays of tumors from 310 patients with breast cancer via immunohistochemistry. In a multivariate Cox regression analysis, a high expression of cofilin in tumor cells correlated significantly with shorter overall survival (hazard ratio, 2.22; 95% confidence interval, 1.35–3.66, P=0.002, and with the Nottingham histologic grade, Ki-67 status and human epidermal growth factor receptor 2 status (P=0.031, 0.001, and 0.001, respectively). Cofilin expression was not observed as correlated with estrogen or progesterone receptor expression, tumor size or lymph node status. These data demonstrate that cofilin is associated with poor outcome, thereby suggesting that it is a potential prognostic factor in breast cancer.
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Affiliation(s)
- Yusufu Maimaiti
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.,Department of General Surgery, Research Institute of Minimally Invasive, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830000, P.R. China
| | - Jie Tan
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zeming Liu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yawen Guo
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yu Yan
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiu Nie
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Bangxing Huang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jing Zhou
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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14
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Faria SS, Morris CFM, Silva AR, Fonseca MP, Forget P, Castro MS, Fontes W. A Timely Shift from Shotgun to Targeted Proteomics and How It Can Be Groundbreaking for Cancer Research. Front Oncol 2017; 7:13. [PMID: 28265552 PMCID: PMC5316539 DOI: 10.3389/fonc.2017.00013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/17/2017] [Indexed: 01/10/2023] Open
Abstract
The fact that cancer is a leading cause of death all around the world has naturally sparked major efforts in the pursuit of novel and more efficient biomarkers that could better serve as diagnostic tools, prognostic predictors, or therapeutical targets in the battle against this type of disease. Mass spectrometry-based proteomics has proven itself as a robust and logical alternative to the immuno-based methods that once dominated the field. Nevertheless, intrinsic limitations of classic proteomic approaches such as the natural gap between shotgun discovery-based methods and clinically applicable results have called for the implementation of more direct, hypothesis-based studies such as those made available through targeted approaches, that might be able to streamline biomarker discovery and validation as a means to increase survivability of affected patients. In fact, the paradigm shifting potential of modern targeted proteomics applied to cancer research can be demonstrated by the large number of advancements and increasing examples of new and more useful biomarkers found during the course of this review in different aspects of cancer research. Out of the many studies dedicated to cancer biomarker discovery, we were able to devise some clear trends, such as the fact that breast cancer is the most common type of tumor studied and that most of the research for any given type of cancer is focused on the discovery diagnostic biomarkers, with the exception of those that rely on samples other than plasma and serum, which are generally aimed toward prognostic markers. Interestingly, the most common type of targeted approach is based on stable isotope dilution-selected reaction monitoring protocols for quantification of the target molecules. Overall, this reinforces that notion that targeted proteomics has already started to fulfill its role as a groundbreaking strategy that may enable researchers to catapult the number of viable, effective, and validated biomarkers in cancer clinical practice.
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Affiliation(s)
- Sara S Faria
- Mastology Program, Federal University of Uberlandia (UFU) , Uberlandia , Brazil
| | - Carlos F M Morris
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Adriano R Silva
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Micaella P Fonseca
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Patrice Forget
- Department of Anesthesiology and Perioperative Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit of Brussel , Brussels , Belgium
| | - Mariana S Castro
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Wagner Fontes
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
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15
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Procházková I, Lenčo J, Fučíková A, Dresler J, Čápková L, Hrstka R, Nenutil R, Bouchal P. Targeted proteomics driven verification of biomarker candidates associated with breast cancer aggressiveness. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:488-498. [PMID: 28216224 DOI: 10.1016/j.bbapap.2017.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/07/2017] [Accepted: 02/15/2017] [Indexed: 02/07/2023]
Abstract
Breast cancer is the most common and molecularly relatively well characterized malignant disease in women, however, its progression to metastatic cancer remains lethal for 78% of patients 5years after diagnosis. Novel markers could identify the high risk patients and their verification using quantitative methods is essential to overcome genetic, inter-tumor and intra-tumor variability and translate novel findings into cancer diagnosis and treatment. We recently identified 13 proteins associated with estrogen receptor, tumor grade and lymph node status, the key factors of breast cancer aggressiveness, using untargeted proteomics. Here we verified these findings in the same set of 96 tumors using targeted proteomics based on selected reaction monitoring with mTRAQ labeling (mTRAQ-SRM), transcriptomics and immunohistochemistry and validated in 5 independent sets of 715 patients using transcriptomics. We confirmed: (i) positive association of anterior gradient protein 2 homolog (AGR2) and periostin (POSTN) and negative association of annexin A1 (ANXA1) with estrogen receptor status; (ii) positive association of stathmin (STMN1), cofilin-1 (COF1), plasminogen activator inhibitor 1 RNA-binding protein (PAIRBP1) and negative associations of thrombospondin-2 (TSP2) and POSTN levels with tumor grade; and (iii) positive association of POSTN, alpha-actinin-4 (ACTN4) and STMN1 with lymph node status. This study highlights a panel of gene products that can contribute to breast cancer aggressiveness and metastasis, the understanding of which is important for development of more precise breast cancer treatment.
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Affiliation(s)
- Iva Procházková
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 65653 Brno, Czech Republic; Masaryk University, Faculty of Science, Department of Biochemistry, Kotlarska 2, 61137 Brno, Czech Republic
| | - Juraj Lenčo
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Trebesska 1575, 50001 Hradec Kralove, Czech Republic
| | - Alena Fučíková
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Trebesska 1575, 50001 Hradec Kralove, Czech Republic
| | - Jiří Dresler
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; Military Health Institute, Tychonova 1, 160 00 Prague, Czech Republic
| | - Lenka Čápková
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 65653 Brno, Czech Republic; Masaryk University, Faculty of Science, Department of Biochemistry, Kotlarska 2, 61137 Brno, Czech Republic
| | - Roman Hrstka
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 65653 Brno, Czech Republic
| | - Rudolf Nenutil
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 65653 Brno, Czech Republic
| | - Pavel Bouchal
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 65653 Brno, Czech Republic; Masaryk University, Faculty of Science, Department of Biochemistry, Kotlarska 2, 61137 Brno, Czech Republic.
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16
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Liu H, Zhang Y, Zheng S, Weng Z, Ma J, Li Y, Xie X, Zheng W. Detention of copper by sulfur nanoparticles inhibits the proliferation of A375 malignant melanoma and MCF-7 breast cancer cells. Biochem Biophys Res Commun 2016; 477:1031-1037. [PMID: 27392714 DOI: 10.1016/j.bbrc.2016.07.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/04/2016] [Indexed: 12/27/2022]
Abstract
Selective induction of cell death or growth inhibition of cancer cells is the future of chemotherapy. Clinical trials have found that cancer tissues are enriched with copper. Based on this finding, many copper-containing compounds and complexes have been designed to "copper" cancer cells using copper as bait. However, recent studies have demonstrated that copper boosts tumor development, and copper deprivation from serum was shown to effectively inhibit the promotion of cancer. Mechanistically, copper is an essential cofactor for mitogen-activated protein kinase (MAPK)/extracellular activating kinase (ERK) kinase (MEK), a central molecule in the BRAF/MEK/ERK pathway. Therefore, depleting copper from cancer cells by directly sequestering copper has a wider field for research and potential for combination therapy. Based on the affinity between sulfur and copper, we therefore designed sulfur nanoparticles (Nano-S) that detain copper, achieving tumor growth restriction. We found that spherical Nano-S could effectively bind copper and form a tighter surficial structure. Moreover, this Nano-S detention of copper effectively inhibited the proliferation of A375 melanoma and MCF-7 breast cancer cells with minimum toxicity to normal cells. Mechanistic studies revealed that Nano-S triggered inactivation of the MEK-ERK pathway followed by inhibition of the proliferation of the A375 and MCF-7 cells. In addition, lower Nano-S concentrations and shorter exposure stimulated the expression of a copper transporter as compensation, which further increased the cellular uptake and anticancer activities of cisplatin. Collectively, our results highlight the potential of Nano-S as an anticancer agent or adjuvant through its detention of copper.
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Affiliation(s)
- Hao Liu
- Department of Chemistry, Jinan University, Guangzhou, China
| | - Yikai Zhang
- Institute of Hematology, Jinan University, Guangzhou, China
| | - Shanyuan Zheng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Zeping Weng
- First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jun Ma
- First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yangqiu Li
- Institute of Hematology, Jinan University, Guangzhou, China; First Affiliated Hospital, Jinan University, Guangzhou, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, 510632, China
| | - Xinyuan Xie
- Department of Chemistry, Jinan University, Guangzhou, China
| | - Wenjie Zheng
- Department of Chemistry, Jinan University, Guangzhou, China.
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17
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Pernikářová V, Bouchal P. Targeted proteomics of solid cancers: from quantification of known biomarkers towards reading the digital proteome maps. Expert Rev Proteomics 2015; 12:651-67. [PMID: 26456120 DOI: 10.1586/14789450.2015.1094381] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The concept of personalized medicine includes novel protein biomarkers that are expected to improve the early detection, diagnosis and therapy monitoring of malignant diseases. Tissues, biofluids, cell lines and xenograft models are the common sources of biomarker candidates that require verification of clinical value in independent patient cohorts. Targeted proteomics - based on selected reaction monitoring, or data extraction from data-independent acquisition based digital maps - now represents a promising mass spectrometry alternative to immunochemical methods. To date, it has been successfully used in a high number of studies answering clinical questions on solid malignancies: breast, colorectal, prostate, ovarian, endometrial, pancreatic, hepatocellular, lung, bladder and others. It plays an important role in functional proteomic experiments that include studying the role of post-translational modifications in cancer progression. This review summarizes verified biomarker candidates successfully quantified by targeted proteomics in this field and directs the readers who plan to design their own hypothesis-driven experiments to appropriate sources of methods and knowledge.
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Affiliation(s)
- Vendula Pernikářová
- a Masaryk University , Faculty of Science, Department of Biochemistry , Kotlářská 2, 61137 Brno , Czech Republic
| | - Pavel Bouchal
- a Masaryk University , Faculty of Science, Department of Biochemistry , Kotlářská 2, 61137 Brno , Czech Republic.,b Masaryk Memorial Cancer Institute , Regional Centre for Applied Molecular Oncology , Žlutý kopec 7, 65653 Brno , Czech Republic
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18
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Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E. A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. J Proteome Res 2015; 14:2807-18. [DOI: 10.1021/acs.jproteome.5b00315] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Ruedi Aebersold
- Department
of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule, 8092 Zurich, Switzerland
| | | | - Emma Niméus
- Division
of Surgery, Skåne University Hospital, 221 85 Lund, Sweden
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19
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Calderón-González KG, Valero Rustarazo ML, Labra-Barrios ML, Bazán-Méndez CI, Tavera-Tapia A, Herrera-Aguirre ME, Sánchez del Pino MM, Gallegos-Pérez JL, González-Márquez H, Hernández-Hernández JM, León-Ávila G, Rodríguez-Cuevas S, Guisa-Hohenstein F, Luna-Arias JP. Determination of the protein expression profiles of breast cancer cell lines by quantitative proteomics using iTRAQ labelling and tandem mass spectrometry. J Proteomics 2015; 124:50-78. [PMID: 25918110 DOI: 10.1016/j.jprot.2015.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/11/2015] [Accepted: 04/13/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED Breast cancer is the principal cancer in women worldwide. Although there are serum tumor markers such as CEA and HER2, they are detected in advanced stages of the disease and used as progression and recurrence markers. Therefore, there is a necessity for the identification of new markers that might lead to an early detection and also provide evidence of an effective treatment. The aim of this work was to determine the differential protein expression profiles of four breast cancer cell lines in comparison to a normal control cell line by iTRAQ labelling and tandem mass spectrometry, in order to identify putative biomarkers of the disease. We identified 1,020 iTRAQ-labelled polypeptides with at least one peptide identified with more than 95% in confidence. Overexpressed polypeptides in all cancer cell lines were 78, whilst the subexpressed were 128. We categorised them with PANTHER program into biological processes, being the metabolic pathways the most affected. We detected six groups of proteins with the STRING program involved in DNA topology, glycolysis, translation initiation, splicing, pentose pathway, and proteasome degradation. The main subexpressed protein network included mitochondrial proteins involved in oxidative phosphorylation. We propose BAG6, DDX39, ANXA8 and COX4 as putative biomarkers in breast cancer. BIOLOGICAL SIGNIFICANCE We report a set of differentially expressed proteins in the MCF7 and T47D (Luminal A), MDA-MB-231 (Claudin low) and SK-BR-3 (HER2(+)) breast cancer cell lines that have not been previously reported in breast cancer disease. From these proteins, we propose BAG6, DDX39, ANXA8 and COX4 as putative biomarkers in breast cancer. On the other hand, we propose sets of unique polypeptides in each breast cancer cell line that can be useful in the classification of different subtypes of breast cancer.
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Affiliation(s)
- Karla Grisel Calderón-González
- Doctorado en Ciencias Biológicas, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, C.P. 09340, México, D. F., México.
| | - Ma Luz Valero Rustarazo
- Unidad de Proteómica, Centro de Investigación Príncipe Felipe, C/Rambla del Saler 16, 46012 Valencia, España.
| | - Maria Luisa Labra-Barrios
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - César Isaac Bazán-Méndez
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Alejandra Tavera-Tapia
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Maria Esther Herrera-Aguirre
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Manuel M Sánchez del Pino
- Unidad de Proteómica, Centro de Investigación Príncipe Felipe, C/Rambla del Saler 16, 46012 Valencia, España.
| | | | - Humberto González-Márquez
- Doctorado en Ciencias Biológicas, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, C.P. 09340, México, D. F., México.
| | - Jose Manuel Hernández-Hernández
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Gloria León-Ávila
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Miguel Hidalgo, C.P. 11340, México, D. F., México.
| | - Sergio Rodríguez-Cuevas
- Instituto de Enfermedades de la Mama, Fundación del Cáncer de Mama (FUCAM A.C.), Av. Bordo No. 100, Col. Viejo Ejido de Santa Ursula Coapa, Coyoacán, C.P. 04980, México, D. F., México.
| | - Fernando Guisa-Hohenstein
- Instituto de Enfermedades de la Mama, Fundación del Cáncer de Mama (FUCAM A.C.), Av. Bordo No. 100, Col. Viejo Ejido de Santa Ursula Coapa, Coyoacán, C.P. 04980, México, D. F., México.
| | - Juan Pedro Luna-Arias
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
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Flodrova D, Benkovska D, Macejova D, Bialesova L, Hunakova L, Brtko J, Bobalova J. Proteomic analysis of changes in the protein composition of MCF-7 human breast cancer cells induced by all-trans retinoic acid, 9-cis retinoic acid, and their combination. Toxicol Lett 2014; 232:226-32. [PMID: 25455455 DOI: 10.1016/j.toxlet.2014.09.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 12/22/2022]
Abstract
Retinoic acid (all-trans and 9-cis) isomers represent important therapeutic agents for many types of cancers, including human breast cancer. Changes in protein composition of the MCF-7 human breast cancer cells were induced by all-trans retinoic acid, 9-cis retinoic acid, and their combination and subsequently proteomic strategies based on bottom-up method were applied. Proposed approach was used for the analysis of proteins extracted from MCF-7 human breast cancer cell line utilizing a commercially manufactured kit RIPA and separated on two dimensional (2D) sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) after treatment with both retinoic acid isomers. We found significant differences in occurrence of proteins probably affecting the cell migration process in tumour cells. Heat shock protein 27, ribonucleoprotein SmD3, and cofilin-1 were significantly upregulated after treatment with combination of individual retinoic acid isomers. On the other hand, AP-5 complex subunit beta-1 shows the different response. Thus, the results might help to find the answer to important medical questions on (i) the identification of signaling pathways affected by retinoic acid isomers or (ii) how the observed proteomic pattern might reflect the effectiveness of retinoic acids treatment.
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Affiliation(s)
- D Flodrova
- Institute of Analytical Chemistry of the ASCR, v. v. i., Brno, Czech Republic
| | - D Benkovska
- Institute of Analytical Chemistry of the ASCR, v. v. i., Brno, Czech Republic
| | - D Macejova
- Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - L Bialesova
- Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - L Hunakova
- Institute of Experimental Oncology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - J Brtko
- Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - J Bobalova
- Institute of Analytical Chemistry of the ASCR, v. v. i., Brno, Czech Republic.
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